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Covalent and non-covalent molecular binding are two strategies to tailor surface properties and functions. However, the lack of responsiveness and requirement for specific binding groups makes spatiotemporal control challenging. Here, we report the adaptive insertion of a hydrophobic anchor into a poly(ethylene glycol) (PEG) host as a non-covalent binding strategy for surface functionalization. By using polycyclic aromatic hydrocarbons as the hydrophobic anchor, hydrophilic charged and non-charged functional modules were spontaneously loaded onto PEG corona in 2 min without the assistance of any catalysts and binding groups. The thermodynamically favourable insertion of the hydrophobic anchor can be reversed by pulling the functional module, enabling programmable surface functionalization. We anticipate that the adaptive molecular recognition between the hydrophobic anchor and the PEG host will challenge the hydrophilic understanding of PEG and enhance the progress in nanomedicine, advanced materials and nanotechnology.

Electron attachment to DNA by low energy electrons can lead to DNA damage, so a fundamental understanding of how electrons interact with the components of nucleic acids in solution is an open challenge. In solution, low energy electrons can generate presolvated electrons, epre-, which are efficiently scavanged by pyrimidine nucleobases to form transient negative ions, able to relax to either stable valence bound anions or undergo dissociative electron detachment or transfer to other parts of DNA/RNA leading to strand breakages. In order to understand the initial electron attachment dynamics, this paper presents a joint molecular dynamics and high-level electronic structure study into the behavior of the electronic states of the solvated uracil anion. Both the valence π* and nonvalence epre- states of the solvated uracil system are studied, and the effect of the solvent environment and the geometric structure of the uracil core are uncoupled to gain insight into the physical origin of the stabilization of the solvated uracil anion. Solvent reorganization is found to play a dominant role followed by relaxation of the uracil core.

The high anisotropy of polymer-based fibres confers them high tensile strength, but also makes them more vulnerable against non-uniform mechanical loads. This is even more important for Kevlar® fib...

Acid/base chemistry is an intriguing topic that still constitutes a challenge for computational chemistry. While estimating the acid dissociation constant (or pKa) could shed light on many chemistry processes, especially in the fields of biochemistry and geochemistry, evaluating the relative stability between protonated and nonprotonated species is often very difficult. Indeed, a prerequisite for calculating the pKa of any molecule is an accurate description of the energetics of water dissociation. Here, we applied constrained molecular dynamics simulations, a noncanonical sampling technique, to investigate the water deprotonation process by selecting the OH distance as the reaction coordinate. The calculation is based on density functional theory and the newly developed SCAN functional, which has shown excellent performance in describing water structure. This first benchmark of SCAN on a chemical reaction shows that this functional accurately models the energetics of proton transfer reactions in an aqueous environment. After taking Coulomb long-range corrections and nuclear quantum effects into account, the estimated water pKa is only 1.0 pKa unit different from the target experimental value. Our results show that the combination of SCAN and constrained MD successfully reproduces the chemistry of water and constitutes a good framework for calculating the free energy of chemical reactions of interest.

Significance The TRPA1 channel functions as an irritant sensor and is a therapeutic target for treating pain, itch, and respiratory diseases. TRPA1 can be activated by electrophilic compounds via covalent modification or activated by noncovalent agonists via ligand binding. However, how covalent modification leads to channel opening and, importantly, how noncovalent binding activates TRPA1 are not well-understood. Here we identified a group of noncovalent agonists and used them to explore TRPA1 gating through iterative functional analyses, molecular modeling, and structure–activity relationship studies. We show that TRPA1 possesses an evolutionarily conserved ligand binding site common to other TRP channels. The combination of computational modeling and experimental structure–activity data lays the foundations for rational drug design., The transient receptor potential ankyrin 1 (TRPA1) channel functions as an irritant sensor and is a therapeutic target for treating pain, itch, and respiratory diseases. As a ligand-gated channel, TRPA1 can be activated by electrophilic compounds such as allyl isothiocyanate (AITC) through covalent modification or activated by noncovalent agonists through ligand binding. However, how covalent modification leads to channel opening and, importantly, how noncovalent binding activates TRPA1 are not well-understood. Here we report a class of piperidine carboxamides (PIPCs) as potent, noncovalent agonists of human TRPA1. Based on their species-specific effects on human and rat channels, we identified residues critical for channel activation; we then generated binding modes for TRPA1–PIPC interactions using structural modeling, molecular docking, and mutational analysis. We show that PIPCs bind to a hydrophobic site located at the interface of the pore helix 1 (PH1) and S5 and S6 transmembrane segments. Interestingly, this binding site overlaps with that of known allosteric modulators, such as A-967079 and propofol. Similar binding sites, involving π-helix rearrangements on S6, have been recently reported for other TRP channels, suggesting an evolutionarily conserved mechanism. Finally, we show that for PIPC analogs, predictions from computational modeling are consistent with experimental structure–activity studies, thereby suggesting strategies for rational drug design.

Purpose To assess whether genotypes at 2 major loci associated with age-related macular degeneration (AMD), complement factor H (CFH), or age-related maculopathy susceptibility 2 (ARMS2), modify the response to oral nutrients for the treatment of AMD in the Age-Related Eye Disease Study 2 (AREDS2). Design Post hoc analysis of a randomized trial. Participants White AREDS2 participants. Methods AREDS2 participants (n = 4203) with bilateral large drusen or late AMD in 1 eye were assigned randomly to lutein and zeaxanthin, omega-3 fatty acids, both, or placebo, and most also received the AREDS supplements. A secondary randomization assessed modified AREDS supplements in 4 treatment arms: lower zinc dosage, omission of β-carotene, both, or no modification. To evaluate the progression to late AMD, fundus photographs were obtained at baseline and annual study visits, and history of treatment for late AMD was obtained at study visits and 6-month interim telephone calls. Participants were genotyped for the single-nucleotide polymorphisms rs1061170 in CFH and rs10490924 in ARMS2. Bivariate frailty models using both eyes were conducted, including a gene–supplement interaction term and adjusting for age, gender, level of education, and smoking status. The main treatment effects, as well as the direct comparison between lutein plus zeaxanthin and β-carotene, were assessed for genotype interaction. Main Outcome Measures The interaction between genotype and the response to AREDS2 supplements regarding progression to late AMD, any geographic atrophy (GA), and neovascular AMD. Results Complete data were available for 2775 eyes without baseline late AMD (1684 participants). The participants (mean age ± standard deviation, 72.1±7.7 years; 58.5% female) were followed up for a median of 5 years. The ARMS2 risk allele was associated significantly with progression to late AMD and neovascular AMD (P = 2.40 × 10–5 and P = 0.002, respectively), but not any GA (P = 0.097). The CFH risk allele was not associated with AMD progression. Genotype did not modify significantly the response to any of the AREDS2 supplements. Conclusions CFH and ARMS2 risk alleles do not modify the response to the AREDS2 nutrient supplements with respect to the progression to late AMD (GA and neovascular AMD).

Purpose To describe the sequence of events leading to development of geographic atrophy (GA) in age-related macular degeneration with fundus autofluorescence (FAF) imaging. Design Post hoc analysis of FAF images from the Age-Related Eye Disease Study 2. Participants Fundus autofluorescence images of 120 eyes (109 patients) with incident GA and at least 2 years of preceding FAF images. Methods Images of incident GA were stacked and aligned over FAF images of preceding annual visits. The regions of retina where incident GA developed were assessed on prior years’ FAF images. These regions, defined as precursor lesions, were classified into minimal change autofluorescence, predominant hypoautofluorescence (decreased autofluorescence), predominant hyperautofluorescence (increased autofluorescence), and mixed autofluorescence. The natural progression in precursor lesions leading to GA formation and their associations with incident GA size and GA enlargement rate were evaluated. Main Outcome Measures Incident GA area and enlargement rate and precursor pattern frequency. Results Incident GA had a mean area of 1.00 mm2 (range, 0.15–8.22 mm2) and an enlargement rate of 0.97 mm2/year (standard deviation, 1.66 mm2/year). Predominant hypoautofluorescence was the most common precursor lesion, increasing from 42% to 81% over 3 years before onset of GA. Almost 30% of eyes showed minimal change autofluorescence 3 years before GA. Among the other precursors, 70% progressed to predominant hypoautofluorescence before GA developed. The type of precursor lesions was not associated with incident GA area. Geographic atrophy evolving from minimal change autofluorescence precursor lesions was associated with faster GA enlargement rates compared with other precursor lesion classes. Conclusions Using image registration, we identified changes in autofluorescence images before the onset of GA. Decreased autofluorescence was the most common change, although minimal changes also were seen in one third of the images. Incident GA that arises from predominantly normal autofluorescence is associated with faster enlargement rates compared with GA arising from abnormal autofluorescence. Faster GA enlargement rates also were associated with incident GA size, area of surround abnormal autofluorescence, and presence of reticular pseudodrusen.

Significance Lipid vesicles are globular assemblies that compartmentalize, encapsulate, transport, and provide signal transmission and communication between cells. In living systems, these vesicles perform critical functions to sustain life. Biomimetic lipid vesicles, such as liposomes, have been developed as mimics of biological cell membranes and for applications in biotechnology, but they do have specific limitations. Dendrimersomes are vesicles self-assembled from amphiphilic Janus dendrimers. They offer improved stability and versatility over liposomes. These dendrimersomes are extremely efficient at loading hydrophobic small molecules and natural macromolecules including folded proteins, at a level higher than comparable liposomes. Additionally, they can be readily functionalized to enable modular recruitment of proteins and nucleic acids on their periphery., Reconstructing the functions of living cells using nonnatural components is one of the great challenges of natural sciences. Compartmentalization, encapsulation, and surface decoration of globular assemblies, known as vesicles, represent key early steps in the reconstitution of synthetic cells. Here we report that vesicles self-assembled from amphiphilic Janus dendrimers, called dendrimersomes, encapsulate high concentrations of hydrophobic components and do so more efficiently than commercially available stealth liposomes assembled from phospholipid components. Multilayer onion-like dendrimersomes demonstrate a particularly high capacity for loading low-molecular weight compounds and even folded proteins. Coassembly of amphiphilic Janus dendrimers with metal-chelating ligands conjugated to amphiphilic Janus dendrimers generates dendrimersomes that selectively display folded proteins on their periphery in an oriented manner. A modular strategy for tethering nucleic acids to the surface of dendrimersomes is also demonstrated. These findings augment the functional capabilities of dendrimersomes to serve as versatile biological membrane mimics.

Halogen bonding has emerged as an important noncovalent interaction in a myriad of applications, including drug design, supramolecular assembly, and catalysis. Current understanding of the halogen bond is informed by electronic structure calculations on isolated molecules and/or crystal structures that are not readily transferable to liquids and disordered phases. To address this issue, we present a first-principles simulation-based approach for quantifying halogen bonds in molecular systems rooted in an understanding of nuclei-nuclei and electron-nuclei spatial correlations. We then demonstrate how this approach can be used to quantify the structure and dynamics of halogen bonds in condensed phases, using solid and liquid molecular chlorine as prototypical examples with high concentrations of halogen bonds. We close with a discussion of how the knowledge generated by our first-principles approach may inform the development of classical empirical models, with a consistent representation of halogen bonding., Comment: 8 pages, 8 figures

Alumina is one of the most abundant minerals and has a wide range of industrial applications, with catalysis as one of the most important. Of particular relevance for catalysis is the structure of the mineral/water interface. In this work, water structure and sodium halide adsorption at the neutral α-alumina(0001)/water interface are investigated using molecular dynamics simulations. This work demonstrates the accuracy of the chosen model of the alumina/water interface and shows that high charge density monovalent ions, such as Na+ and F–, have a strong affinity for the interface due to the specific pattern of alumina surface OH groups, such that the adsorbed ions displace waters that are hydrogen-bonded to the surface in their absence. A significant portion of the driving force for anion adsorption arises from surface bound Na+, which reverse the intrinsic surface dipole field and drive the accumulation of halides at the interface. The resulting electrolytic interfacial structure reorients water molecule...

We present a new model for the calculation of molecular polarizabilities from effective atomic polarizabilities. This model is based on the Thole modified dipole interaction model for molecular polarizabilities, where the total polarizability is computed as a sum of effective atomic polarizabilities modified by dipole-dipole interactions. We extend this model by making the atomic polarizabilities explicit functions of the interatomic distances, scaling them by the radius of the volume an atom occupies in a molecule. We use the SCAN functional to show that this model, denoted TholeL, yields accurate molecular polarizabilities with little dependence on the training set. We also demonstrate that the TholeL model yields accurate polarizabilities for configurations far from the ground state structure for a wide range of molecules. Finally, we show that the TholeL model can be used to generate accurate Raman spectra for water, crystalline urea, and urea in water from ab initio molecular dynamics simulations.

Summary Store-operated calcium release-activated calcium (CRAC) channels mediate a variety of cellular signaling functions. The CRAC channel pore-forming protein, Orai1, is a hexamer arranged with 3-fold symmetry. Despite its importance in moving Ca2+ ions into cells, a detailed mechanistic understanding of Orai1 activation is lacking. Herein, a working model is proposed for the putative open state of Orai from Drosophila melanogaster (dOrai), which involves a “twist-to-open” gating mechanism. The proposed model is supported by energetic, structural, and experimental evidence. Fluorescent imaging demonstrates that each subunit on the intracellular side of the pore is inherently strongly cross-linked, which is important for coupling to STIM1, the pore activator, and graded activation of the Orai1 channel. The proposed model thus paves the way for understanding key aspects of calcium signaling at a molecular level., Graphical Abstract, Highlights • Mechanical coupling within the calcium channel pore is critical for its activation • Molecular modeling could disclose gating mechanism of ion channels at atomic level • The predicted open-state structure of the pore was further confirmed by experiments, Biological Sciences; Molecular Biology; Structural Biology

The lowering of reaction overpotentials is a persistent and universal goal in the development of catalysts for (photo)electrochemistry, which can usually be facilitated by selectively stabilizing one reaction intermediate over another. In this mechanistic study of the oxygen evolution reaction (OER) catalyzed by cobalt-intercalated layered MnO2, we show that confinement effects and local cobalt atomic ordering in the interlayer space can be synergistically used to tune the adsorption energies of O, OH, and OOH reaction intermediates and the scaling relationship between them. In general, the interlayer confinement destabilizes the adsorption of intermediates for the OER, but clustering Co atoms can selectively stabilize the adsorption of OOH in particular. After considering both effects, our model predicts an overpotential of 0.30 V for the Co-intercalated MnO2 catalyzed OER, in excellent agreement with the experimental result of 0.36 V. These new insights explain the enhanced catalytic performance of MnO2 by intercalating atoms and illuminate a route for engineering non-toxic precious-metal-free catalysts through designed layered materials.

The intercalation of Co in NiFe layered double hydroxides (LDH) significantly improves the electrocatalytic performance of the LDH for the oxygen evolution reaction. The mechanism behind the improv...

Oxide–water interfaces are ubiquitous, with many applications in industry and the environment, yet there is a great deal of controversy over their properties and microscopic structure. This controversy stems, in part, from the unique H-bond networks formed at different surface terminations and mineral compositions. Density functional theory simulations of these interfaces require an accurate description of both the oxide mineral and water in diverse H-bond environments. Thus, herein we simulate the Al2O3(001)–H2O interface using the PBE, PBE-TS, RPBE, SCAN, and HSE06-TS functionals to determine how calculated interfacial properties depend on the choice of functional. We find that the structure of the first few layers of water at the surface is determined by electron correlation in a way that cannot be approximated using semiemipirical van der Waals corrections. Of the functionals investigated, we find that SCAN yields the most accurate interfacial structure, dynamics, and sum frequency generation spectrum...

Water exchange reactions around ionic solutes are ubiquitous in aqueous solution-phase chemistry. However, the extreme sensitivity of exchange rates to perturbations in the chemistry of an ionic solute is not well understood. We examine water exchange around model ions within the language of dynamic facilitation theory, typically used to describe glassy and other systems with collective, facilitated dynamics. Through the development of a coarse-grained, kinetically-constrained lattice model of water exchange, we show that the timescale for water exchange scales exponentially with the strength of the solute-solvent interactions., Comment: 8 pages, 6 figures

Development of inexpensive and efficient photo- and electro-catalysts is vital for clean energy applications. Electronic and structural properties can be tuned by the introduction of defects to achieve the desirable electrocatalytic activity. Using first-principles molecular dynamics simulations, the structural, dynamical, and electronic properties of 2D borocarbonitride (h-BCN) sheets have been investigated, highlighting how anti-site defects in B and N doped graphene significantly influence the bandgap, and thereby open up new avenues to tune the chemical behavior of the 2D sheets. In the present work, all of the monolayers investigated display direct bandgaps, which reduce from 0.99 eV to 0.24 eV with increasing number of anti-site defects. The present results for the electronic structure and findings for bandgap engineering open up applications of BCN monolayers in optoelectronic devices and solar cells. The influence of the anti-site distribution of B and N atoms on the ultra-high hole/electron mobility and conductivity is discussed based on density functional theory coupled with the Boltzmann transport equation. The BCN defect monolayer is predicted to have carrier mobilities three times higher than that of the pristine sheet. The present results demonstrate that BN doped graphene monolayers are likely to be useful in the next-generation 2D field-effect transistors.

SARS-CoV-2 has raised the alarm to search for effective therapy for this virus. To date several vaccines have been approved but few available drugs reported recently still need approval from FDA. Remdesivir was approved for emergency use only. In this report, the SARS-CoV-2 3CLpro was expressed and purified. By using a FRET-based enzymatic assay, we have screened a library consisting of more than 300 different niclosamide derivatives and identified three molecules JMX0286, JMX0301, and JMX0941 as potent allosteric inhibitors against SARS-CoV-2 3CLpro, with IC

This chapter returns to Kristeva’s early work on intertextuality in ‘The Bounded Text’ (1968) to show that her focus was on ideology and subjectivity, particularly the way that literature contributes to the ‘bourgeois social text’. The chapter argues that there are two conceptions of intertextuality: the first involves the common practice of seeking allusions and quotations; the second involves the typology of a text and its contribution to a bourgeois subjectivity. This second type of intertextuality plays a role in the post-human conception of the subject that Kristeva arguably borrows (with alterations) from Lacan. This conception views the subject as formed in advance by language, although Kristeva veers from Lacan in her insistence that poetic language (Revolution in Poetic Language) can develop despite the control of the symbolic, creating a new kind of literature and subjectivity. The chapter argues that the open intertextuality of works like Foss’s Baroque Variations does not lead to a new subjectivity. Turning to earlier modernism, the chapter looks particularly at Ravel’s Violin Sonata No. 2, to argue that a new kind of subjectivity attempts to form itself in the open typology of its topics and conventions.

21 p.-4 fig., Glycan-lectin recognition is vital to processes that impact human health including viral infections. Proceeding from crystallographical evidence of case studies on adeno-, corona- and rotaviral spike proteins, the relationship of these adhesins to mammalian galectins was examined by computational similarity assessments. Intrafamily diversity among human galectins was in the range of that to these viral surface proteins. Our findings are offered to inspire the consideration of lectin-based approaches to thwart infection by present and future viral threats, also mentioning possible implications for vaccine development., We gratefully acknowledge inspiring discussions with Drs. B. Friday, A. Leddoz and A. W. L. Nose, the valuable input by the three reviewers and support from European Cooperation in Science and Technology (COST) Action CA18103 (InnoGly). V.P. and M.L.K. are thankful for generous support of the P. Roy Vagelos Chair at UPenn and the Sheikh Saqr Foundation, RAK, respectively

Currently the entire human population is in the midst of a global pandemic caused by SARS-CoV-2 (Severe Acute Respiratory Syndrome CoronaVirus 2). This highly pathogenic virus has to date caused >71 million infections and >1.6 million deaths in >180 countries. Several vaccines and drugs are being studied as possible treatments or prophylactics of this viral infection. M3CLpro (coronavirus main cysteine protease) is a promising drug target as it has a significant role in viral replication. Here we use the X-ray crystal structure of M3CLpro in complex with boceprevir to study the dynamic changes of the protease upon ligand binding. The binding free energy was calculated for water molecules at different locations of the binding site, and molecular dynamics (MD) simulations were carried out for the M3CLpro/boceprevir complex, to thoroughly understand the chemical environment of the binding site. Several HCV NS3/4a protease inhibitors were tested in vitro against M3CLpro. Specifically, asunaprevir, narlaprevir, paritaprevir, simeprevir, and telaprevir all showed inhibitory effects on M3CLpro. Molecular docking and MD simulations were then performed to investigate the effects of these ligands on M3CLpro and to provide insights into the chemical environment of the ligand binding site. Our findings and observations are offered to help guide the design of possible potent protease inhibitors and aid in coping with the COVID-19 pandemic.

Summary The small 3-O-sulfated galactose head group of sulfatides, an abundant glycosphingolipid class, poses the (sphinx-like) riddle on involvement of glycan bridging by tissue lectins (sugar code). First, synthesis of head group derivatives for functionalization of amphiphilic dendrimers is performed. Aggregation of resulting (biomimetic) vesicles, alone or in combination with lactose, demonstrates bridging by a tissue lectin (galectin-4). Physiologically, this can stabilize glycolipid-rich microdomains (rafts) and associate sulfatide-rich regions with specific glycoproteins. Further testing documents importance of heterobivalency and linker length. Structurally, sulfatide recognition by galectin-8 is shown to involve sphingosine's OH group as substitute for the 3′-hydroxyl of glucose of lactose. These discoveries underscore functionality of this small determinant on biomembranes intracellularly and on the cell surface. Moreover, they provide a role model to examine counterreceptor capacity of more complex glycans of glycosphingolipids and to start their bottom-up glycotope surface programming., Graphical abstract, Highlights • Nanoparticle programming detects sulfatide-(N)-glycan bridging by galectins-4 and -8 • Protein design (linker/domain type) is a switch for aggregation activity • Sphingosine's OH group is involved in contact building with a galectin, Supramolecular Chemistry; Biochemistry; Biophysics

ADAP1/Centaurin-α1 (CentA1) functions as an Arf6 GTPase-activating protein highly enriched in the brain. Previous studies demonstrated the involvement of CentA1 in brain function as a regulator of dendritic differentiation and a potential mediator of Alzheimer’s disease pathogenesis. To better understand the neurobiological functions of CentA1 signaling in the brain, we developed Centa1 knockout mice. The knockout animals showed neither brain development nor synaptic ultrastructure deficits in the hippocampus. However, they exhibited significantly higher density and enhanced structural plasticity of dendritic spines in the CA1 region of the hippocampus compared to non-transgenic littermates. Moreover, the deletion of Centa1 improved performance in the object-in-place spatial memory task. These results suggest that CentA1 functions as a negative regulator of spine density and plasticity, and of hippocampus-dependent memory formation. Thus, CentA1 and its downstream signaling may serve as a potential therapeutic target to prevent memory decline associated with aging and brain disorders. SIGNIFICANCE STATEMENT ADAP1/Centaurin-α1 (CentA1) is highly enriched in the brain and has been shown to be involved in the developmental regulation of dendritic differentiation. Although increased CentA1 level has been linked to Alzheimer’s disease, the underlying neurological mechanisms are unknown. We found that the genetic deletion of Centa1 leads to increased dendritic spine plasticity and enhanced spine structural plasticity in the hippocampus, accompanied by behavioral improvements in a location recognition task. This is the first study of CentA1 role in the brain, and our findings will facilitate the understanding of neurobiological mechanisms underlying the regulation of dendritic spine morphology and plasticity in healthy brains and in neurological disorders.

Path-integral ab initio molecular dynamics (PI-AIMD) calculations have been employed to probe the nature of chloride ion solvation in aqueous solution. Nuclear quantum effects (NQEs) are shown to weaken hydrogen bonding between the chloride anion and the solvation shell of water molecules. As a consequence, the disruptive effect of the anion on the solvent water structure is significantly reduced compared to what is found in the absence of NQEs. The chloride hydration structure obtained from PI-AIMD agrees well with information extracted from neutron scattering data. Inparticular, the observed satellite peak in the hydrogen-chloride-hydrogen triple angular distribution serves as a clear signature of NQEs. The present results suggest that NQEs are likely to play acrucial role in determining the structure of saline solutions., 6 pages, 4figures

Unlike metal or semiconductor electrodes, the surface charge resulting from the protonation or deprotonation of insulating mineral oxides is highly localized and heterogeneous in nature. In this work the Stark active C≡N stretch of potassium thiocyanate is used as a molecular probe of the heterogeneity of the interfacial electrostatic potential at the α-Al

Poly($p$-phenylene terephthalamide) (PPTA) exhibits van der Waals (vdW) bonding along its $a$ axis, hydrogen bonding along its $b$ axis, and covalent bonding along its $c$ axis. We explore the structural and mechanical properties of PPTA using density functional theory with various functionals including LDA, PBE, PBE+rVV10L, SCAN, and SCAN+rVV10, compared with available experiments. The hierarchy of nonempirical semilocal functionals LDA, PBE, and SCAN (not fitted to any multicenter bonded system) includes differing amounts of intermediate-range vdW interaction. rVV10 is the long-range vdW correction. (rVV10L differs from rVV10 only in the value of a range parameter.) Among the tested functionals, SCAN shows the best performance for the lattice parameters of PPTA along the two crystal directions involving vdW or hydrogen-bond interaction. The equilibrium lattice constants obtained by SCAN and PBE+rVV10L are closest to experimental data, while SCAN+rVV10 slightly overbinds the system. We study the mechanical response of PPTA by applying strain along three lattice directions. Due to the inclusion of vdW interaction, SCAN, PBE+rVV10L, and SCAN+rVV10 all exhibit correct bonding strain-energy curves. On the contrary, PBE strongly underestimates the vdW interaction needed to resist uniaxial stretching along the $a$ axis. The Young's modulus and yield strength of PPTA are computed and compared with previous results. The experimental values are much smaller than the computed ones, mainly due to the fact that the PPTA fiber samples used for measurements are mechanically weaker than the perfect molecular crystals considered in the simulations. Interestingly, when a compressive uniaxial stress of 25 Kbar is applied along the $b$ axis, a structural phase transition, in which the hydrogen bonds reform along one diagonal of the $ab$ rectangle, is predicted by SCAN.

This chapter discusses the central term of its title: intertextuality, a term coined by Kristeva which means any allusion or quotation from one text in another. In literature, intertextuality leads readers to discover that the meaning of a work involves looking outward to another work. The same process of looking outside the work is involved with musical topics, which are conventions of musical meaning. As conventions, topics open a musical work to other works. The essay uses Melville’s Moby-Dick and Chopin’s Polonaise-Fantaisie as examples. The implication of intertextuality in literature and in music is that a single work cannot be interpreted without references to works outside the one at hand. Thus every literary and music work is always open during interpretation, never reaching a fixed point.

This chapter considers the extent to which the joint discipline of literature and music constitutes a separate area of study. The essay begins with a consideration of the origins of literature and music separately as areas of scholarly study. The modern study of literature is a product of the nineteenth-century devotion to an ideology of moral values. The modern study of music comes from the same period, with a focus on Bildung, the aesthetic and moral development of the modern citizen. The shared focus and historical time period of these areas of study is less suggestive than the fact that literature is always resorting to music, and music is always using literature (the song being the most obvious example). To illustrate how the two disciplines might become one, the essay examines two scenes in literature that involve music: one from David Mitchell’s Cloud Atlas, and another from George Eliot’s Middlemarch.

The mechanism of action of quaternary ammonium compound (QAC) antiseptics has long been assumed to be straightforward membrane disruption, although the process of approaching and entering the membrane has little modeling precedent. Furthermore, questions have more recently arisen regarding bacterial resistance mechanisms, and why select classes of QACs (specifically, multicationic QACs) are less prone to resistance. In order to better understand such subtleties, a series of molecular dynamics simulations were utilized to help identify these molecular determinants, directly comparing mono-, bis-, and triscationic QACs in simulated membrane intercalation models. Three distinct membranes were simulated, mimicking the surfaces of Escherichia coli and Staphylococcus aureus, as well as a neutral phospholipid control. By analyzing the resulting trajectories in the form of a timeseries analysis, insight was gleaned regarding the significant steps and interactions involved in the destabilization of phospholipid bilayers within the bacterial membranes. Finally, to more specifically probe the effect of the hydrophobic section of the amphiphile that presumably penetrates the membrane, a series of alkyl- and ester-based biscationic quaternary ammonium compounds were prepared, tested for antimicrobial activity against both Gram-positive and Gram-negative bacteria, and modeled.

Traditional classifications of crystalline phases focus on nuclear degrees of freedom. Through examination of both electronic and nuclear structure, we introduce the concept of an electronic plastic crystal. Such a material is classified by crystalline nuclear structure, while localized electronic degrees of freedom - here lone pairs - exhibit orientational motion at finite temperatures. This orientational motion is an emergent phenomenon arising from the coupling between electronic structure and polarization fluctuations generated by collective motions, such as phonons. Using ab initio molecular dynamics simulations, we predict the existence of electronic plastic crystal motion in halogen crystals and halide perovskites, and suggest that such motion may be found in a broad range of solids with lone pair electrons. Such fluctuations in the charge density should be observable, in principle via synchrotron scattering., Comment: 5 pages, 2 figures

The specificity of aqueous halide solvation is fundamental to a wide range of bulk and interfacial phenomena spanning from biology to materials science. Halide polarizability is thought to drive the ion specificity, and if so, it is essential to have an accurate description of the electronic properties of halide ions in water. To this end, the solvation of the chloride anion, Cl− has been reinvestigated with state-of-the-art density functional theory. Specifically, the PBE-D3, PBE0-D3, and SCAN functionals have been employed to probe the impact of correlation and exchange approximations. Anticipating the findings, adding exact exchange improves the electronic structure, but simultaneously significantly reduces the Cl− polarizability, resulting in an over-structured Cl–O radial distribution function (RDF) and longer water H-bond lifetimes to Cl−. SCAN does not yield as much improvement in the energetics of Cl− relative to bulk water, but does result in a smaller reduction of the polarizability and thus a less structured Cl–O RDF, which agrees better with experiment. Special consideration is therefore warranted in assessing the impact of exchange on the energy, charge density, and the charge density response when designing and testing hybrid functionals for aqueous halide solvation.

This study demonstrates that monodisperse entangled polymer melts crystallize via the formation of nanoscale nascent polymer crystals (i.e., nuclei) that exhibit substantial variability in terms of their constituent crystalline polymer chain segments (stems). More specifically, large-scale coarse-grain molecular simulations are used to quantify the evolution of stem length distributions and their properties during the formation of polymer nuclei in supercooled prototypical polyethylene melts. Stems can adopt a range of lengths within an individual nucleus (e.g., &sim, 1&ndash, 10 nm) while two nuclei of comparable size can have markedly different stem distributions. As such, the attainment of chemically monodisperse polymer specimens is not sufficient to achieve physical uniformity and consistency. Furthermore, stem length distributions and their evolution indicate that polymer crystal nucleation (i.e., the initial emergence of a nascent crystal) is phenomenologically distinct from crystal growth. These results highlight that the tailoring of polymeric materials requires strategies for controlling polymer crystal nucleation and growth at the nanoscale.

Many atomic liquids can form transient covalent bonds reminiscent of those in the corresponding solid states. These directional interactions dictate many important properties of the liquid state, necessitating a quantitative, atomic-scale understanding of bonding in these complex systems. A prototypical example is liquid silicon, wherein transient covalent bonds give rise to local tetrahedral order and consequent non-trivial effects on liquid state thermodynamics and dynamics. To further understand covalent bonding in liquid silicon, and similar liquids, we present an ab initio simulation-based approach for quantifying the structure and dynamics of covalent bonds in condensed phases. Through the examination of structural correlations among silicon nuclei and maximally localized Wannier function centers, we develop a geometric criterion for covalent bonds in liquid Si. We use this to monitor the dynamics of transient covalent bonding in the liquid state and estimate a covalent bond lifetime. We compare covalent bond dynamics to other processes in liquid Si and similar liquids and suggest experiments to measure the covalent bond lifetime., Comment: 6 pages, 4 figures

Sorsby Fundus Dystrophy (SFD) is a rare form of macular degeneration that is clinically similar to age-related macular degeneration (AMD), and a histologic hallmark of SFD is a thick layer of extracellular deposits beneath the retinal pigment epithelium (RPE). Previous studies of SFD patient-induced pluripotent stem cell (iPSC) derived RPE differ as to whether these cultures recapitulate this key clinical feature by forming increased drusenoid deposits. The primary purpose of this study is to examine whether SFD patient-derived iPSC-RPE form basal deposits similar to what is found in affected family member SFD globes and to determine whether SFD iPSC RPE may be more oxidatively stressed. We performed a careful comparison of iPSC RPE from three control individuals, multiple iPSC clones from two SFD patients’ iPSC RPE, and post-mortem eyes of affected SFD family members. We also examined the effect of CRISPR-Cas9 gene correction of the S204C TIMP3 mutation on RPE phenotype. Finally, targeted metabolomics analysis with liquid chromatography and mass spectrometry analysis and stable isotope-labeled metabolite analysis was performed to determine whether SFD RPE are more oxidatively stressed. We found that SFD iPSC-RPE formed significantly more sub-RPE deposits (∼6-90 μm in height) compared to control RPE at 8 weeks. These deposits were similar in composition to the basal laminar drusen found in SFD family member globes by immunofluorescence staining and TEM imaging. S204C TIMP3 correction by CRISPR-Cas9 gene editing in SFD iPSC RPE cells resulted in significantly reduced basal laminar and sub-RPE calcium deposits. We detected a ∼18-fold increase in TIMP3 accumulation in the extracellular matrix (ECM) of SFD RPE, and targeted metabolomics showed that intracellular 4-hydroxyproline, a major breakdown product of collagen, is significantly elevated in SFD RPE, suggesting increased ECM turnover. Finally, SFD RPE cells have decreased intracellular reduced glutathione and were found to be more vulnerable to oxidative stress. Our findings suggest that elements of SFD pathology can be demonstrated in culture which may lead to insights into disease mechanisms.

Significance Gram-negative bacterial cells such as Escherichia coli contain a relatively rigid outer membrane, and cross-linked peptidoglycan in their periplasm, giving them the rigidity and stability to survive independently in harsh environments. To dismantle these strong bacterial cell envelopes, enzymatic processes need to be used. In contrast, human cell membranes are much more fragile, making it possible to dismantle them more easily by relatively mild mechanical disruption. Once these membranes are dismantled, they can be coassembled with synthetic phospholipid mimics, named Janus dendrimers, into cell-like hybrids. This method stabilizes the delicate human cell membranes, introducing the potential for the study of human cell membranes and of their constituents in vitro in a more robust environment., Cell-like hybrids from natural and synthetic amphiphiles provide a platform to engineer functions of synthetic cells and protocells. Cell membranes and vesicles prepared from human cell membranes are relatively unstable in vitro and therefore are difficult to study. The thicknesses of biological membranes and vesicles self-assembled from amphiphilic Janus dendrimers, known as dendrimersomes, are comparable. This feature facilitated the coassembly of functional cell-like hybrid vesicles from giant dendrimersomes and bacterial membrane vesicles generated from the very stable bacterial Escherichia coli cell after enzymatic degradation of its outer membrane. Human cells are fragile and require only mild centrifugation to be dismantled and subsequently reconstituted into vesicles. Here we report the coassembly of human membrane vesicles with dendrimersomes. The resulting giant hybrid vesicles containing human cell membranes, their components, and Janus dendrimers are stable for at least 1 y. To demonstrate the utility of cell-like hybrid vesicles, hybrids from dendrimersomes and bacterial membrane vesicles containing YadA, a bacterial adhesin protein, were prepared. The latter cell-like hybrids were recognized by human cells, allowing for adhesion and entry of the hybrid bacterial vesicles into human cells in vitro.

Purpose To analyze the prevalence, incidence, and clinical characteristics of eyes with geographic atrophy (GA) in age-related macular degeneration (AMD), including clinical and genetic factors affecting enlargement. Design Prospective cohort study within a controlled clinical trial. Participants Age-Related Eye Disease Study 2 (AREDS2) participants, aged 50–85 years. Methods Baseline and annual stereoscopic color fundus photographs were evaluated for GA presence and area. Analyses included GA prevalence and incidence rates, Kaplan-Meier rates, mixed-model regression, and multivariable analysis of the square root of GA, area adjusted for covariates, including clinical/imaging characteristics and genotype. Main Outcome Measures (1) Presence or development of GA; (2) change in the square root of GA area over time. Results At baseline, 517 eyes (6.2%) of 411 participants (9.8%) had pre-existing GA (without neovascular AMD), with the following characteristics: 33% central, 67% noncentral; and the following configurations: 36% small, 26% solid/unifocal, 24% multifocal, 9% horseshoe/ring, and 6% indeterminate. Of the remaining 6530 eyes at risk, 1099 eyes (17.3%) of 883 participants developed incident GA without prior neovascular disease during mean follow-up of 4.4 years. The Kaplan-Meier rate of incident GA was 19% of eyes at 5 years. In eyes with incident GA, 4-year risk of subsequent neovascular AMD was 29%. In eyes with incident noncentral GA, 4-year risk of central involvement was 57%. GA enlargement rate (following square root transformation) was similar in eyes with pre-existing GA (0.29 mm/year; 95% confidence interval 0.27–0.30) and incident GA (0.28 mm/year; 0.27–0.30). In the combined group, GA enlargement was significantly faster with noncentrality, multifocality, intermediate baseline size, and bilateral GA (P Conclusions Analyses of AREDS2 data on natural history of GA provide representative data on GA evolution and enlargement. GA enlargement, which was influenced by lesion features, was relentless, resulting in rapid central vision loss. The genetic variants associated with faster enlargement were partially distinct from those associated with risk of incident GA. These findings are relevant to further investigations of GA pathogenesis and clinical trial planning.

We use density functional theory molecular dynamics simulations to investigate the structure, dynamics, and vibrational sum frequency generation (vSFG) spectra at the Al2O3(0001)–H2O and Al2O3(1120)–H2O interfaces. We find that the differences in the vSFG spectra between the two interfaces can be explained by significantly weaker surface–water interactions at the (0001) vs (1120) interface. The weaker interactions at the (0001) surface are caused by the flat surface plane and high density of OH groups, leading to a decoupling of the vibrational modes of the surface OH groups and H2O molecules. The (0001) vSFG spectrum thus displays two well-separated peaks at the near-neutral pH, in contrast to the vSFG spectrum of the corrugated (1120) interface, which has stronger surface–water interactions and thereby a narrower band in the vSFG spectrum with closely spaced peaks. By simulating the interfaces with both the Perdew–Burke–Ernzerhof (PBE)–Tkatchenko–Scheffler and revised PBE (RPBE) functionals, we find ...

General anesthetics inhibit voltage-gated sodium channels by unknown molecular mechanisms. Using computation-guided NMR and electrophysiology analyses, Wang et al. show that propofol binds to the prokaryotic sodium channel NaChBac at multiple distinct sites., Voltage-gated sodium (NaV) channels are important targets of general anesthetics, including the intravenous anesthetic propofol. Electrophysiology studies on the prokaryotic NaV channel NaChBac have demonstrated that propofol promotes channel activation and accelerates activation-coupled inactivation, but the molecular mechanisms of these effects are unclear. Here, guided by computational docking and molecular dynamics simulations, we predict several propofol-binding sites in NaChBac. We then strategically place small fluorinated probes at these putative binding sites and experimentally quantify the interaction strengths with a fluorinated propofol analogue, 4-fluoropropofol. In vitro and in vivo measurements show that 4-fluoropropofol and propofol have similar effects on NaChBac function and nearly identical anesthetizing effects on tadpole mobility. Using quantitative analysis by 19F-NMR saturation transfer difference spectroscopy, we reveal strong intermolecular cross-relaxation rate constants between 4-fluoropropofol and four different regions of NaChBac, including the activation gate and selectivity filter in the pore, the voltage sensing domain, and the S4–S5 linker. Unlike volatile anesthetics, 4-fluoropropofol does not bind to the extracellular interface of the pore domain. Collectively, our results show that propofol inhibits NaChBac at multiple sites, likely with distinct modes of action. This study provides a molecular basis for understanding the net inhibitory action of propofol on NaV channels.

Solid, liquid and alloyed phases of gallium play a role in a variety of important technological applications. While many of the gallium phases involved in these applications are metallic, some have...

The in vitro antidiabetic and antihyperlipidemic activities of an alcoholic extract of Trigonella stellata were evaluated in terms of the activation of PPARα and PPARγ in human hepatoma (HepG2) cells. The extract was investigated phytochemically, aiming at the isolation of the most active compounds to be used as a platform for drug discovery. Three new isoflavans, (3S,4R)-4,2′,4′-trihydroxy)-7-methoxyisoflavan (1), (3R,4S)-4,2′,4′-trihydroxy-7-methoxy-4′-O-β-d-glucopyranosylisoflavan (2), and (2S,3R,4R)-4,2′,4′-trihydroxy-2,7-dimethoxyisoflavan (3), were isolated and characterized along with the five known compounds p-hydroxybenzoic acid (4), 7,4′-dihydroxyflavone (5), dihydromelilotoside (6), quercetin-3,7-O-α-l-dirhamnoside (7), and soyasaponin I (8). The structures of 1–3 were elucidated using various spectroscopic techniques including HRESIMS and 1D and 2D NMR. The absolute stereochemistry of the new isoflavans (1–3) was determined using both experimental and calculated electronic circular dichroism a...

We report the observation of a sizable photostrictive effect of 5.7% with fast, submillisecond response times, arising from a light-induced lattice dilation of a molecular nanosheet, composed of the molecular charge-transfer compound dibenzotetrathiafulvalene (DBTTF) and C60. An interfacial self-assembly approach is introduced for the thickness-controlled growth of the thin films. From photoabsorption measurements, molecular simulations, and electronic structure calculations, we suggest that photostriction within these films arises from a transformation in the molecular structure of constituent molecules upon photoinduced charge transfer, as well as the accommodation of free charge carriers within the material. Additionally, we find that the photostrictive properties of the nanosheets are thickness-dependent, a phenomenon that we suggest arises from surface-induced conformational disorder in the molecular components of the film. Moreover, because of the molecular structure in the films, which results largely from interactions between the constituent π-systems and the sulfur atoms of DBTTF, the optoelectronic properties are found to be anisotropic. This work enables the fabrication of 2D molecular charge-transfer nanosheets with tunable thicknesses and properties, suitable for a wide range of applications in flexible electronic technologies.

The conformational stability of synthesized diphenyloxalohydrazide and dibenzoyloxalohydrazide fluoro derivatives has been investigated by extensive NMR studies that are ascertained by various levels of theoretical calculations. Two-dimensional 1H–19F HOESY NMR experiments revealed the close spatial proximity between two NMR-active nuclei, confirming the hydrogen bond (HB)-mediated interaction between them, further aiding in establishing the probable stable conformations of these molecules. The relaxed potential energy scan disclosed the energy-minimized most stable structure among the several possible multiple conformations, which is in concurrence with NMR interpretations. Atomistic molecular dynamics simulations have been employed to unequivocally establish the conformational stability and the nature of HB formation at varied temperatures. With the possibility of occurrence of a number of probable conformations, the percentage of occurrences of different types of HBs in them was determined by MD simula...